+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1c4r | ||||||
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タイトル | THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING | ||||||
要素 | NEUREXIN-I BETA | ||||||
キーワード | MEMBRANE PROTEIN (膜タンパク質) / LECTIN-LIKE (レクチン) / NEUROBIOLOGY (神経科学) / CELL-CELL ADHESION (細胞接着) / CELL-CELL RECOGNITION / ALTERNATIVE SPLICING (選択的スプライシング) | ||||||
機能・相同性 | 機能・相同性情報 protein-containing complex assembly involved in synapse maturation / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding ...protein-containing complex assembly involved in synapse maturation / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / cerebellar granule cell differentiation / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / synapse maturation / negative regulation of filopodium assembly / maintenance of synapse structure / vocal learning / positive regulation of synapse maturation / neuroligin family protein binding / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic membrane adhesion / synaptic vesicle clustering / regulation of postsynaptic density assembly / inhibitory synapse / receptor localization to synapse / neuron cell-cell adhesion / regulation of grooming behavior / presynapse assembly / regulation of synaptic vesicle cycle / protein localization to synapse / NMDA glutamate receptor clustering / vocalization behavior / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / neurotransmitter secretion / regulation of AMPA receptor activity / filopodium assembly / neuron maturation / acetylcholine receptor binding / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / adult behavior / positive regulation of protein kinase A signaling / regulation of NMDA receptor activity / social behavior / calcium channel regulator activity / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / regulation of presynapse assembly / excitatory synapse / endocytic vesicle / GABA-ergic synapse / prepulse inhibition / axonal growth cone / presynaptic active zone membrane / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / 学習 / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / 概日リズム / calcium-dependent protein binding / neuron projection development / transmembrane signaling receptor activity / presynaptic membrane / positive regulation of peptidyl-serine phosphorylation / chemical synaptic transmission / 血管新生 / 核膜 / vesicle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / signaling receptor binding / neuronal cell body / glutamatergic synapse / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / 細胞膜 / 小胞体 / シグナル伝達 / protein-containing complex / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 解像度: 2.6 Å | ||||||
データ登録者 | Rudenko, G. / Nguyen, T. / Chelliah, Y. / Sudhof, T.C. / Deisenhofer, J. | ||||||
引用 | ジャーナル: Cell(Cambridge,Mass.) / 年: 1999 タイトル: The structure of the ligand-binding domain of neurexin Ibeta: regulation of LNS domain function by alternative splicing. 著者: Rudenko, G. / Nguyen, T. / Chelliah, Y. / Sudhof, T.C. / Deisenhofer, J. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1c4r.cif.gz | 275.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1c4r.ent.gz | 226.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1c4r.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c4/1c4r ftp://data.pdbj.org/pub/pdb/validation_reports/c4/1c4r | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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-要素
#1: タンパク質 | 分子量: 19693.072 Da / 分子数: 8 / 断片: EXTRACELLULAR DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / プラスミド: PGEX-KG / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q63373 #2: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 2 |
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-試料調製
結晶 | マシュー密度: 3.75 Å3/Da / 溶媒含有率: 67.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 6.5 / 詳細: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 21 ℃ / pH: 7.5 / 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 110 K | |||||||||||||||
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放射光源 | 由来: シンクロトロン / サイト: SSRL / ビームライン: BL1-5 / 波長: 1.0712, 0.9791, 0.9793, 0.9221 | |||||||||||||||
放射 | プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | |||||||||||||||
放射波長 |
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反射 | Biso Wilson estimate: 29.3 Å2 | |||||||||||||||
反射 | *PLUS 最高解像度: 2.6 Å / 最低解像度: 20 Å / Num. obs: 73128 / % possible obs: 98.1 % / Num. measured all: 351083 / Rmerge(I) obs: 0.095 | |||||||||||||||
反射 シェル | *PLUS 最高解像度: 2.6 Å / 最低解像度: 2.64 Å / % possible obs: 82.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.1 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.6→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 38.87 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 38.2 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.6→20 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.5 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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